Resolution and b value dependent structural connectome in ex vivo mouse brain.

Area of Science:

• Neuroimaging
• Biomedical Engineering
• Computational Neuroscience

Background:

• Diffusion MRI (dMRI) is crucial for mapping tissue microstructure and brain connectivity in clinical and preclinical research.
• Existing dMRI protocols, like those from the Human Connectome Project (HCP), are optimized for humans but less explored in preclinical rodent models.
• High-quality dMRI datasets are essential for accurate structural connectome reconstruction, particularly in small animal models like mice.

Purpose of the Study:

• To acquire and characterize high-quality, high-resolution dMRI datasets of ex vivo mouse brains using a 9.4T system.
• To systematically investigate the impact of key acquisition parameters (b-value, angular resolution, spatial resolution) on structural connectome outcomes.
• To provide guidelines for optimizing dMRI acquisition strategies in preclinical rodent studies.

Main Methods:

• Acquisition of dMRI datasets from mouse brains using a 9.4T MRI system from two vendors.
• Acquisition of a unique high-spatial resolution dataset (25 µm isotropic, 126 directions) and a high-angular resolution dataset (50 µm isotropic, 384 directions).
• Systematic investigation of b-values (1000–8000 s/mm²), angular resolution (10–126 directions), and spatial resolution (25–200 µm) effects on tractography and connectome metrics.

Main Results:

• Tractography stability and connectome accuracy significantly improve with angular resolution, with over 50 diffusion encoding directions being critical for consistent results.
• A linear relationship (R² > 0.99) was observed between connectome parameters and b-values, indicating that single-shell acquisitions at 3000 s/mm² can yield results comparable to multi-shell data.
• Decreased spatial resolution led to a lower Dice coefficient and increased false positive and false negative rates in connectome reconstruction.

Conclusions:

• This study establishes foundational guidelines for optimizing dMRI acquisition parameters in ex vivo mouse brains for structural connectome mapping.
• Trade-offs between spatial resolution, angular resolution, and b-value are critical for balancing data quality, acquisition time, and connectome accuracy.
• The findings support the development of efficient and effective dMRI protocols for preclinical neuroscience research.